Hi John,
a few answers, maybe Jorge has more details when he get’s back from travel.
1. if you look at the wiki: Y = M(:,7:9), therefore these are the left and right hippo-volumes. So the plot shows the total hippocampal volume.
2. I think you need to plot them individually. Probably you won’t see anything anyway if it is plotted on top of each other. You can sum left+right if you like or look at hemispheres independently.
3. There should be as many lines as groups. I am not sure about the order. The script uses a call to ‘unique' to find unique groups, so I guess it is the order in which groups appear in the qdec file. The order of the colors is: colors = {'b','k','g','c','m','r','y’}; (it starts with ‘k’ and wraps around at the end) Take a look at the lme_lowessPlot.m file, it should be easy to add a legend to the plot, by copying and editing the file.
4. that parameter smoothes the data. It calls smooth with the ‘rlowess’ parameter. See the help of ‘smooth' or play around with the parameter. The goal of the plot is to see a trend of the data, so smooth away small bumps but not the main signal.
Best, Martin
On Jan 2, 2016, at 10:57 AM, John Anderson j.anderson@publicist.com wrote:
Hi Freesurfer experts, I am working on a logitudinal data analysis using freesurfer pipeline. I followed all the steps like in WIKI and the analysis was great. Kindly I have the following questions:
- In wiki "http://freesurfer.net/fswiki/LinearMixedEffectsModels http://freesurfer.net/fswiki/LinearMixedEffectsModels"-- in the example mentioned there, the command "
lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2));" What is the Y(:,2) refer to ? 2. Can I plot multiple measures at the same time ( for example if I have in my qdec table multiple columns for multiple measures ( left precentral gyrus cortical thickness, right precentral gyrus cortical thickness, LH mean thickness , RH mean thickness) can I plot all these measures at the same time instead of running the previous command multiple times? 3. If I have three groups in my qdec table. The previous command line is plotting three lines. Are these lines in th esame order of the groups in qdec tables? 4. The BW in this command was chosen 0.7 and the default is 0.6 how can I choose this number correctly?
Thanks for your support!
Bests, John Anderson
Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer